I aligned a BAC contig (assembled from sanger sequences) to a reference genome using BWA-mem. The output alignments are very similar to the best end to end alignment I got from aligning the bac contig to the reference with Blat.
But how do I now interpret the alignments made by BWA-mem as SNP's, InDels and SV's that the BAC contig has versus the reference?
SNP's and InDels are kind of obvious to see in the data. But because the alignment of the BAC contig is given as multiple separate alignments it is kind of hard to see what is going on SV wise.
I want to use the variants gathered from the BAC sequence to estimate a FN and FP rate for the same strain sequenced and variant called with short read data.